Step-by-step Instructions for using the pdb_extract webserver

pdb_extract can be used to convert PDB format files to PDBx/mmCIF format and is a vital resource for the submission of large structures. You will be offered the option of using a template file containing data that can be shared among several depositions.

  1. Go to
  2. Browse to find the coordinate file to be converted.
  3. Select the appropriate file type. Note: PDB or PDBx/mmCIF files can be used as input.
  4. Select one of the three different methods (X‐Ray, NMR, and EM).
    • X-ray is fully supported for all of the current crystallographic applications including neutron and X-ray/neutron hybrids. Normally, PDB file REMARK 200 (data collection for X-ray) and REMARK 230 (data collection for Neutron) are not present in uploaded PDB model files, but pdb‐extract has a data template file that can describe the data collection. The extracted data will be combined with the templates and merged into one model PDBx/mmCIF file.
    • The NMR option is also fully supported, but only limited statistics can be extracted from the log files of three programs (CNS, CYANA, and DYANA). A data template file (for the author, and experiment conditions) is also provided.
    • The EM option is supported only for transferring sequences into the entity_poly category. Again a data template file is available.
  5. Click "Run." For EM, the "Select Program for Structure Refinement" option can be ignored.
  6. If your coordinate file has no chain-IDs, pdb_extract will stop and ask you to provide them.
  7. If pdb_extract detects any formatting or data errors, it will provide instructions for fixing them. After they are fixed, the first steps can be repeated.
  8. If everything is ok after you click the run button, you will get a second webpage titled "Extracting Information for PDB Deposition." This new page contains various sections depending on the experimental method. A help file is provided at the top of the page.
    • Section 1, "Information about Authors, Detectors…" provides a template that can be used for inserting various data items into the extracted PDBx/mmCIF file. This is optional, as the information it provides can also be entered easily via the deposition interface.
    • Sections 2, 3, and 4 are primarily for X‐ray diffraction experiments and are also optional. These sections provide the options to convert structure factors to PDBx/mmCIF format, extract information from various steps of structure determination and provide or verify the unit cell parameters.
    • Section 5 of the "Extracting Information for PDB Deposition" page provides macromolecular sequence information that has been extracted from the provided coordinate file. If the input file was a PDB file containing SEQRES records, sequences will be taken preferentially from that section. Otherwise, the sequence information will be extracted directly from the model coordinates themselves. The user can then review and edit each sequence and its associated chain ID and polymer type. Please note the following points:
      • Sequence information extracted by pdb_extract is automatically read into the wwPDB Deposition System. It is therefore important to correct all issues with sequence at this stage.
      • Missing, concatenated, or otherwise unusual sequence information presented on the “Extracting Information for PDB Deposition” page may indicate the presence of data or formatting errors in the original coordinates that were not directly detected by pdb_extract. Please review these sequences carefully.
      • The extracted sequence information should be corrected to include all residues of each unique biopolymer, including any unmodeled terminal regions or gaps. Sequences extracted from coordinates will contain stretches of question marks ("????") where gaps were detected in the sequence. These may be the result of missing residues or bad geometry. These should be replaced with the correct experimental sequence.
  9. Press "Run." On the next page, a link will be available for downloading the extracted PDBx/mmCIF format file (pdb_extract_coord_xxxx.cif).
  10. The file(s) are now ready for deposition. To deposit the structure to the wwPDB, please go to: